| Input Elements | Output Elements | ||
| PlateView | Manipulate samples |
Heatmap | Overview of all samples and probes |
| Experiment Table |
Manipulate experiments |
Bargraph |
Show probes and/or samples |
| Sample
Table |
Manipulate samples |
Differential Expression
Table |
Show p-value ranked
differential expression |
| Probe
Table |
Manipulate probes |
Variable Data Chart |
Show selected probes broken
out by group |
| Variable Table |
Manipulate variables |
Volcano
Plot |
Show p-value / fold
expression chart |
| Pair
Plot |
Compare a pair of probes or
samples |
Stability
Plot |
Probe suitability for
normalization |
| Buttons | Other
actions |
||
| Load
Button |
Bring data from disk into
memory |
Menus |
The top menu bar |
| Experiment Button |
Create experiments |
FDE |
Quick access to the Firefly
Discovery Engine |
| Negative Button |
Mark negative samples |
Selection | Selecting probes, samples, experiments |
| Normalize Button |
Toggle normalization status |
Zoom & pan | Moving around charts |
| Export
Button |
Save data from memory back
to disk |
Tables |
General info about tables |
| Clear
Button |
Empty memory |
Variable Definition |
How to define variables |
| Features
and modes |
Switching assay or feature
level |
||
| Files | Concepts |
||
| FCS file | Flow cytometry data | Work flow | Samples vs plates vs experiments |
| FWS file | Firefly workspace | Experiment | Group of samples for statistical processing |
| PLX
file |
Barcoded probe definition |
Plate | Group of samples for visual selection |
| Sample
Sheet |
Plate layout definition |
Variable | Basis for differential analysis |
Standard Curve |
Quantification using known standards |
LoD | Limit of detection |
| Sample quality | Data quality in a particular sample | ||
| Data
Processing |
Calculating target levels
in each sample from flow cytometry events |
| Data Statistics |
How the mean, standard
deviation and confidence intervals are calculated |
| Normalization |
Motivation, algorithms and
experience with normalization |
| Clustering |
Hierarchical clustering
used to organize the heatmap |
| Differential Analysis |
Using variables to analyze
differential expression between groups of samples |
| Multiple Comparisons |
Calculating p-values in a
multiplex context |
| Anova with repeated measures |
Differential analysis of a
primary variable, controlling for secondary variables. |
| Standard Curves |
Absolute quantitation using
known standards |
| Extended Range |
Rescuing a dataset with
saturated signal |
| Scripting
with Python |
How to write Python scripts
to process data |